Gemmatimonas phototrophica AP64 is the first phototrophic representative of bacterial phylum Gemmatimonadetes. The cells contain photosynthetic complexes with bacteriochlorophyll a as the main light-harvesting pigment. In addition, the complexes contain a carotenoid with a single broad absorption band at 490 nm in methanol. A combination of nuclear magnetic resonance, high-resolution mass spectroscopy and Fourier-transformed infra-red spectroscopy was used to determine the chemical structure of G. phototrophica light-harvesting carotenoid that we have named gemmatoxanthin. It is a novel linear carotenoid containing 11 conjugated double bonds and further substituted by methoxy, carboxyl and aldehyde group. Its IUPAC-IUBMB semi-systematic name is 1’-Methoxy-19’-oxo-3’,4’-didehydro-7,8,1’,2’-tetrahydro- Ψ, Ψ carotene-16-oic acid. To our best knowledge, the presence of the carboxyl, methoxy and aldehyde groups on a linear C40 carotenoid backbone is reported here for the first time.